A chemotactic-based model for spatial activity recognition

Spatial activity recognition in everyday environments is particularly challenging due to noise incorporated during video-tracking. We address the noise issue of spatial recognition with a biologically inspired chemotactic model that is capable of handling noisy data. The model is based on bacterial chemotaxis, a process that allows bacteria to survive by changing motile behaviour in relation to environmental dynamics. Using chemotactic principles, we propose the chemotactic model and evaluate its classification performance in a smart house environment. The model exhibits high classification accuracy (99%) with a diverse 10 class activity dataset and outperforms the discrete hidden Markov model (HMM). High accuracy (>89%) is also maintained across small training sets and through incorporation of varying degrees of artificial noise into testing sequences. Importantly, unlike other bottom–up spatial activity recognition models, we show that the chemotactic model is capable of recognizing simple interwoven activities

A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments

Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments—including ground and surface waters—from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the β-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth

Use of Proteomics Tools to Investigate Protein Expression in Azospirillum brasilense

Mass spectrometry based proteomics has emerged as a powerful methodology for investigating protein expression. “Bottom up” techniques in which proteins are first digested, and resulting peptides separated via multi-dimensional chromatography then analyzed via mass spectrometry provide a wide depth of coverage of expressed proteomes. This technique has been successfully and extensively used to survey protein expression (expression proteomics) and also to investigate proteins and their associated interacting partners in order to ascertain function of unknown proteins (functional proteomics). Azospirillum brasilense is a free-living diazotrophic soil bacteria, with world-wide significance as a plant-growth promoting bacteria. Living within the rhizosphere of cereal grasses, its diverse metabolism is important for its survival in the competitive rhizospheric environment. The recently sequenced genome of strain Sp245 provided a basis for the proteome studies accomplished in this work. After initial mass spectrometer parameter optimization studies, the expressed proteomes of two strains of Azospirillum brasilense, Sp7 and Sp245, grown under both nitrogen fixing and optimal growth (non nitrogen fixing) conditions were analyzed using a bottom up proteomics methodology. Further proteome studies were conducted with A. brasilense strain Sp7 in order to ascertain the effect of one chemotaxis operon, termed Che1. In this study, proteomic surveys were conducted on two bacterial derivative strains, created earlier, which lacked either a forward signaling pathway or an adaptation pathway. The proteomic surveys conducted in this work provide a foundation for further biochemical investigations. In order to facilitate further investigation and a movement into functional proteomics, a set of destination vectors was created that contain a variety of tandem affinity tags. The addition of tandem affinity tags to a protein allow for generic purification schemes, and can facilitate future studies to investigate proteins of interest discovered in the first expression proteomic surveys of A. brasilense. Taken together, this dissertation provides a valuable data set for investigation into the physiology of A. brasilense and further provides biochemical tools for analysis of the functional protein interactions of A. brasilense cells

Tools for Quantifying Bacterial Motility Using Digital Holographic Microscopy as Applied to Studying the Simulated Microgravity Environment

Digital holographic microcopy (DHM) is a label-free technique that has gained attention in recent years as a tool for volumetric imaging. One application of DHM is for the study of microbial motility with the advantage being that organisms may freely move within their environment. Images created from DHM are in the form of holograms. Holograms are time recordings showing XY information with the Z information contained within. Z information can be retrieved from the holograms directly through a variety of numerical techniques or through reconstruction. Datasets generated from DHM are large and processing remains a challenging task. Here, we show how following reconstruction, the refocusing method can be used to locate particles manually through Z. We note the difference between the lateral and axial resolutions and show the impact of the point-spread functions on resolving data. We show that 2D tracking of organisms is generally sufficient for quantifying motility though specific applications such as surface behavior still require 3D information. With this understanding, we shift to studying the microgravity environment. The microgravity environment is the weightless environment of the space station. It is difficult to conduct experiments on the space station, so we simulate certain characteristics of that environment on Earth by using simulated microgravity devices. We review bacterial responses to microgravity and the simulated microgravity environment with an emphasis on motility and chemotaxis. Finally, we apply the techniques developed in this thesis to study the simulated microgravity environment by examining the motility and chemotaxis of Vibrio alginolyticus. We show that while there was little change in motility between simulated microgravity and normal gravity, there is a statistically significant difference in cloud sizes. Future work would involve comparing these responses with the actual microgravity environment

Absolute quantification of microbial proteomes at different states by directed mass spectrometry

The developed, directed mass spectrometry workflow allows to generate consistent and system-wide quantitative maps of microbial proteomes in a single analysis. Application to the human pathogen L. interrogans revealed mechanistic proteome changes over time involved in pathogenic progression and antibiotic defense, and new insights about the regulation of absolute protein abundances within operons